Fluorophore structure

One Lucifer Yellow derivative is available for labeling sulfhydryl-containing molecules. Lucifer Yellow iodoacetamide is a 4-ethyliodoacetamide derivative of the basic disulfonate aminonaph-thalimide fluorophore structure (Invitrogen). The iodoacetyl groups react with —SH groups in proteins and other molecules to form stable thioether linkages (Figure 9.42). 

Photoluminescence (PL) in the polysilanes is well documented,34b,34c and for the poly(diarylsilane)s occurs typically with a small Stokes shift and almost mirror image profile of the UV absorption.59 This is due to the similarity of the chromophore and fluorophore structures in the ground and excited states, respectively, which is a result of the fact that little structural change occurs on excitation of the electrons from the a to the a orbitals. As PL is the emissive counterpart to UV, the emissive counterpart to CD is circularly polarized pho-toluminescence (CPPL). Where the fluorophore is chiral, then the photoexcited state can return to the ground state with emission of circularly polarized light, the direction of polarization of which depends on the relative intensities of the right-handed and left-handed emissions (/R and /l, respectively), which in turn depends on the chirality of the material, or more accurately, the chirality... 

The broad emission and low-fluorescence quantum yield of PPS suggested a distribution of trapping sites in the Si skeleton, which were also considered responsible for the lower-than-expected conductivity. The far-IR spectrum of PPS suggested the existence of cyclohexasilane rings connected by linear chains.361,362 Subsequent investigations by Irie et al. on the electronic absorption spectra of radical ions of poly(alkylsilyne)s were taken to indicate the presence of various cyclic silicon species, in corroboration of this conclusion.363 The large Stokes shift and broadness of the fluorescence emission indicate a range of fluorophore structures, different from the chromophore structures. This is... 

The first pH indicators studied possessed the acid-base site (phenol, aniline, or carboxylic acid) as an integral part of the fluorophore. Structurally, in the most general sense, pH sensitivity is due to a reconfiguration of the fluorophorets re-electron system that occurs on protonation. Consequently, the acid and the base forms often show absorption shifts and also, when the two forms fluoresce, emission shifts or at least, when only one form emits, a pH-dependent fluorescence intensity. This class of compounds has been reviewed 112 and the best structures have to be designed according to the medium probed and the technique used. After a short consideration of physiological pH indicators we will describe the main photophysical processes sensible to protonation. 

Students should read carefully the whole text before beginning the experiments and plotting the spectra. The purpose of these experiments is to find out how the fluorophore structure affects optical spectroscopy properties such as absorbance and fluorescence. 

Y. Zhang, K. Aslan, M. J. Previte, and C. D. Geddes. Metal-Enhanced Fluorescence Surface Plasmons can Radiate a Fluorophores Structured Emission Applied Physics Letters, 2007, 90, 053107. 

Intensity, position of the emission wavelength, lifetime are some observables that are going to characterize a fluorophore. Modification of the temperature and / or the viscosity of the medium will affect the values of these observables. Each fluorophore has its own fluorescence properties and observables. These properties are intrinsic to the fluorophore and are modified with the environment. We shall see in the next chapter that these modifications do not follow the same rules for all fluorophores. Therefore, it is important to understand the nature of the fluorophore environment before taking conclusions that could be misleading in the interpretation of the studied phenomenon. Also, we are going to see that fluorophore structure can influence its fluorescence lifetimes. This will vary from a fluorophore to another. 

Naylor, B. L. Picardo, M. Homan, R. Pownall, H. J. Effects of fluorophore structure andhydrophobicity on the uptake and metabolism of fluorescent lipid analogs. Chetn. Phys. Lipids 1991,58,111-119. 

Structure of GFP and its chromophore. To study the chro-mophore of GFP, a sample of GFP was denatured by heating it at 90°C. It was digested with papain, and then a peptide containing the fluorophore was isolated and purified from the digested mixture. The structural study of the peptide has indicated that the chromophore of GFP is an imidazolone derivative shown below (Shimomura, 1979). This chromophore structure was confirmed later by Cody etal. (1993) in a hexapeptide isolated from GFP. It is intriguing that the structure of the GFP chromophore is a part of the structure of coelenterazine. 

Applications of the oxalate-hydrogen peroxide chemiluminescence-based and fluorescence-based assays with NDA/CN derivatives to the analysis of amino acids and peptides are included. The sensitivity of the chemiluminescence and fluorescence methods is compared for several analytes. In general, peroxyoxalate chemiluminescence-based methods are 10 to 100 times more sensitive than their fluorescence-based counterparts. The chief limitation of chemiluminescence is that chemical excitation of the fluorophore apparently depends on its structure and oxidation potential. 

Fluorescence probes possessing the PyU base 46 selectively emit fluorescence only when the complementary base is adenine. In this case, the chromophore of is extruded to the outside of the duplex because of Watson-Crick base pair formation, and exposed to a highly polar aqueous phase. On the contrary, the duplex containing a PyU/N (N = G, C and T) mismatched base pair shows a structure in which the glycosyl bond of uridine is rotated to the syn conformation. In this conformation, the fluorophore is located at a hydrophobic site of the duplex. The control of base-specific fluorescence emission is based on the polarity change in the microenvironment where the fluorophore locates are dependent on the l>yU/A base-pair formation. 

Based on the preliminary understanding of ICT mechanism of coumarin core skeleton, the first systematic application of combinatorial approach toward the field of fluorescence chemistry was reported by Bauerle and co-workers in 2001 [44]. In their study, the structure-photophysical property relationships (SPR) of coumarin fluorophore were revealed by means of a combinatorial approach. 

The tunability on emission wavelength of cyanine derivatives is based on the understanding of structure-photophysical property relationships, which allows the development of near-IR fluorophores [80, 84—87]. Enhancement of the rigidity in... 

Fig. 26 (a) Monomer structures of oligodeoxyfluorosides (ODF) library, (b) Photophysical properties of ODF fluorophores. Reproduced with permission from [94]... 

Exciplexes are complexes of the excited fluorophore molecule (which can be electron donor or acceptor) with the solvent molecule. Like many bimolecular processes, the formation of excimers and exciplexes are diffusion controlled processes. The fluorescence of these complexes is detected at relatively high concentrations of excited species, so a sufficient number of contacts should occur during the excited state lifetime and, hence, the characteristics of the dual emission depend strongly on the temperature and viscosity of solvents. A well-known example of exciplex is an excited state complex of anthracene and /V,/V-diethylaniline resulting from the transfer of an electron from an amine molecule to an excited anthracene. Molecules of anthracene in toluene fluoresce at 400 nm with contour having vibronic structure. An addition to the same solution of diethylaniline reveals quenching of anthracene accompanied by appearance of a broad, structureless fluorescence band of the exciplex near 500 nm (Fig. 2 )... 

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